Contacts of the helix formed by residues 854 - 875 (chain C) in PDB entry 6UZA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 854 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C GLU* 3.7 20.1 - - - +
351C GLU* 4.3 17.6 + - - +
853C ARG* 1.3 77.7 - - - +
855C TYR* 1.3 61.0 + - - +
857C LYS* 3.3 27.1 + - - +
858C ILE* 3.0 44.4 + - + +
861C ARG* 4.9 5.2 + - - +
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Residues in contact with TYR 855 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C GLU 6.1 0.2 - - - -
292C ASP* 2.9 38.8 + - + -
344C ALA* 3.6 36.1 + - + -
348C GLY 3.9 15.7 - - - -
349C ASP* 3.3 45.3 - - + +
350C VAL 5.5 0.4 - - - +
351C GLU* 4.7 4.2 + - - +
365C ARG* 3.5 11.6 + - - -
853C ARG* 3.5 13.7 - - - +
854C GLN* 1.3 79.0 - - - +
856C GLN* 1.3 64.0 + - - +
858C ILE* 3.5 4.8 + - - -
859C MET* 2.9 50.3 + - + +
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Residues in contact with GLN 856 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C GLU* 3.5 35.3 + - - +
853C ARG* 3.1 62.3 + - + +
854C GLN 3.3 0.4 - - - -
855C TYR* 1.3 83.4 - - - +
857C LYS* 1.3 57.2 + - + +
859C MET* 3.9 5.2 - - - +
860C LYS* 2.9 31.3 + - - +
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Residues in contact with LYS 857 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853C ARG 3.4 17.0 + - - +
854C GLN* 3.3 29.9 + - - +
855C TYR 3.3 0.4 - - - -
856C GLN* 1.3 79.1 - - + +
858C ILE* 1.3 57.8 + - - +
860C LYS* 3.3 7.1 + - - +
861C ARG* 3.0 39.8 + - - +
212D ASP* 3.9 30.4 + - - +
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Residues in contact with ILE 858 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C GLU* 3.6 43.7 - - + +
341C GLU* 4.0 15.5 - - + -
344C ALA* 3.7 25.8 - - + -
854C GLN* 3.0 36.3 + - + +
855C TYR* 4.0 4.5 - - - +
857C LYS* 1.3 75.1 - - - +
859C MET* 1.3 58.3 + - - +
861C ARG* 3.4 20.6 + - + +
862C LEU* 3.0 42.3 + - + +
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Residues in contact with MET 859 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C GLU 4.9 10.5 - - - +
292C ASP* 3.9 9.0 - - - +
293C PRO* 3.8 33.0 - - + -
294C VAL* 4.2 13.7 - - + -
332C LEU* 4.7 5.2 - - + -
344C ALA* 4.4 5.4 - - - +
345C ILE* 4.0 22.2 - - + -
855C TYR* 2.9 55.7 + - + +
856C GLN* 4.1 6.3 - - - +
858C ILE* 1.3 74.9 - - - +
860C LYS* 1.3 58.0 + - - +
862C LEU* 3.4 8.4 + - + +
863C ILE* 2.9 39.5 + - + +
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Residues in contact with LYS 860 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856C GLN 2.9 20.0 + - - +
857C LYS* 3.7 7.0 - - - +
858C ILE 3.3 0.2 - - - -
859C MET* 1.3 77.7 - - - +
861C ARG* 1.3 57.0 + - - +
863C ILE* 3.4 5.0 + - - -
864C LYS* 3.0 27.5 + - - +
86D TYR* 5.3 11.0 - - - +
88D PHE* 3.7 20.9 - - + -
89D SER 3.2 28.8 + - - +
90D ASP* 4.2 15.8 + - - +
91D ARG 5.8 0.2 - - - -
92D SER* 5.4 5.3 - - - -
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Residues in contact with ARG 861 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C ASN* 4.0 5.7 - - - +
340C GLU* 3.9 19.2 + - - -
341C GLU* 3.6 17.0 + - - -
854C GLN* 4.9 4.6 + - - +
857C LYS* 3.0 25.9 + - - +
858C ILE* 3.4 27.3 - - - +
860C LYS* 1.3 75.8 - - - +
862C LEU* 1.3 63.8 + - + +
864C LYS* 3.4 7.0 + - - +
865C ARG* 3.0 57.9 + - - +
209D TYR* 5.5 0.3 + - - -
210D ASP* 5.6 4.3 - - - +
212D ASP* 3.0 50.7 + - - +
213D GLY* 5.4 7.5 - - - -
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Residues in contact with LEU 862 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C LEU* 3.9 16.9 - - + +
335C LEU* 4.3 13.6 - - + +
336C CYS* 4.2 14.8 - - - -
341C GLU* 3.6 14.6 - - + +
345C ILE* 3.8 31.9 - - + -
858C ILE* 3.0 39.6 + - + +
859C MET* 3.9 9.9 - - + +
860C LYS 3.3 0.4 - - - -
861C ARG* 1.3 77.8 - - + +
863C ILE* 1.3 59.9 + - - +
865C ARG* 3.4 30.9 + - - +
866C TYR* 2.9 28.1 + - - +
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Residues in contact with ILE 863 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C SER* 3.4 33.7 - - - +
288C LEU* 5.3 0.2 - - + -
290C SER 4.9 4.3 - - - +
291C GLU 4.6 6.5 - - - +
293C PRO* 3.8 37.0 - - + -
328C PHE* 6.1 0.4 - - + -
332C LEU* 5.1 5.2 - - + -
859C MET* 2.9 28.0 + - + +
860C LYS* 3.9 5.4 - - - +
862C LEU* 1.3 74.4 - - - +
864C LYS* 1.3 59.5 + - - +
866C TYR* 3.2 6.7 + - - +
867C VAL* 3.0 31.3 + - + +
86D TYR* 6.0 4.0 - - + -
88D PHE* 3.8 28.9 - - + -
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Residues in contact with LYS 864 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860C LYS* 3.0 17.6 + - + +
861C ARG* 3.8 7.0 - - - +
862C LEU 3.3 0.2 - - - -
863C ILE* 1.3 78.1 - - - +
865C ARG* 1.3 62.3 + - - +
867C VAL* 3.4 3.1 + - - +
868C LEU* 3.0 33.5 + - + +
88D PHE* 3.7 24.4 - - + -
90D ASP* 4.8 4.1 - - + +
132D MET* 2.7 37.1 + - - +
133D GLY* 4.0 6.1 + - - -
134D GLN* 4.3 4.8 - - - +
209D TYR* 3.6 36.8 + - - +
210D ASP* 2.5 44.4 + - - +
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Residues in contact with ARG 865 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LEU* 3.0 40.1 + - + -
337C ARG* 3.7 42.4 - - - +
338C ASN* 5.3 0.4 - - - +
341C GLU* 2.4 46.3 + - - -
861C ARG* 3.0 39.7 + - - +
862C LEU* 3.5 16.2 - - - +
863C ILE 3.4 0.2 - - - -
864C LYS* 1.3 75.5 - - - +
866C TYR* 1.3 58.2 + - - +
868C LEU* 4.1 4.7 - - - +
869C GLN* 2.9 33.3 + - - +
209D TYR* 4.7 11.7 - - - +
214D THR 5.1 1.9 + - - +
215D ARG 5.7 2.2 - - - +
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Residues in contact with TYR 866 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C TYR* 4.0 10.9 + - - -
283C PRO* 3.7 23.0 - - + +
287C SER* 4.3 13.0 - - - -
327C ASP 5.1 0.7 + - - -
328C PHE* 3.5 46.7 - + - -
331C GLY* 4.1 21.3 - - - -
332C LEU* 3.8 17.9 - - + -
335C LEU* 3.7 20.4 - - + +
862C LEU 2.9 17.3 + - - +
863C ILE* 3.2 7.4 + - - +
865C ARG* 1.3 75.5 - - - +
867C VAL* 1.3 59.5 + - - +
869C GLN* 4.1 2.1 - - + +
870C ALA* 2.9 36.8 + - + +
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Residues in contact with VAL 867 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C TYR* 4.0 28.4 - - + -
287C SER* 4.4 8.7 - - - +
288C LEU* 4.3 19.7 - - + -
863C ILE* 3.0 27.2 + - + +
864C LYS* 3.4 5.4 + - - +
865C ARG 3.3 0.2 - - - -
866C TYR* 1.3 77.3 - - - +
868C LEU* 1.3 57.7 + - + +
870C ALA* 3.4 5.5 + - - +
871C GLN* 3.0 50.5 + - - +
88D PHE* 5.0 1.1 - - + -
132D MET* 3.8 26.0 - - + -
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Residues in contact with LEU 868 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864C LYS* 3.0 26.9 + - + +
865C ARG* 4.1 4.0 - - - +
867C VAL* 1.3 77.8 - - - +
869C GLN* 1.3 57.7 + - - +
871C GLN* 3.4 18.5 + - - +
872C ILE* 3.0 37.4 + - + +
132D MET* 3.8 27.8 - - + -
134D GLN* 4.5 8.1 - - - +
209D TYR* 3.8 37.0 - - + +
215D ARG* 4.1 19.5 - - + +
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Residues in contact with GLN 869 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LEU* 4.2 22.9 - - + +
865C ARG 2.9 18.8 + - - +
866C TYR* 4.1 3.1 - - + +
868C LEU* 1.3 76.0 - - - +
870C ALA* 1.3 56.8 + - - +
872C ILE* 3.3 21.7 + - - +
873C ASP* 2.9 59.8 + - - +
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Residues in contact with ALA 870 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C TYR* 3.3 35.4 - - + +
866C TYR* 2.9 28.7 + - + +
867C VAL 3.7 1.8 - - - +
869C GLN* 1.3 75.0 - - - +
871C GLN* 1.3 60.4 + - - +
873C ASP* 3.4 7.6 + - - +
874C LYS* 2.9 30.0 + - - +
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Residues in contact with GLN 871 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C TYR* 3.8 27.8 - - + +
233C GLU* 5.0 1.2 - - - +
867C VAL* 3.0 40.1 + - - +
868C LEU* 3.8 16.4 - - - +
869C GLN 3.3 0.2 - - - -
870C ALA* 1.3 73.1 - - - +
872C ILE* 1.3 61.2 + - + +
874C LYS* 3.3 11.9 + - - +
875C GLU* 3.0 36.8 + - + +
131D TYR* 4.1 17.2 + - - -
132D MET* 5.2 2.1 - - - +
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Residues in contact with ILE 872 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868C LEU* 3.0 26.4 + - + +
869C GLN* 3.6 23.3 - - - +
871C GLN* 1.3 77.1 - - + +
873C ASP* 1.3 69.2 + - - +
875C GLU* 3.2 19.7 + - - +
876C SER* 3.5 16.3 + - - +
167D LEU* 6.5 0.7 - - + -
171D LYS* 6.4 0.9 - - - +
215D ARG* 6.1 3.4 - - - +
216D PHE* 6.4 1.8 - - + -
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Residues in contact with ASP 873 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869C GLN* 2.9 47.1 + - - +
870C ALA* 3.9 6.7 - - - +
872C ILE* 1.3 78.7 - - - +
874C LYS* 1.3 61.2 + - - +
876C SER* 3.4 18.8 + - - -
877C ASP* 4.0 11.3 - - - +
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Residues in contact with LYS 874 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C CYS 5.6 2.5 - - - +
230C GLN* 2.6 37.9 + - + +
231C GLU* 4.6 5.7 + - - +
232C TYR* 3.3 29.5 - - - +
870C ALA 2.9 16.5 + - - +
871C GLN* 3.7 14.4 - - - +
872C ILE 3.3 0.2 - - - -
873C ASP* 1.3 75.5 - - - +
875C GLU* 1.3 59.1 + - + +
876C SER 3.1 5.0 + - - -
877C ASP* 3.7 17.6 + - - +
881D GLU* 3.1 28.9 - - - +
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Residues in contact with GLU 875 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871C GLN* 3.0 20.5 + - - +
872C ILE* 3.2 13.4 + - - +
874C LYS* 1.3 78.1 - - + +
876C SER* 1.3 57.5 + - - -
877C ASP 3.7 0.7 - - - -
171D LYS* 4.3 15.8 + - - -
880D ASN* 3.6 8.0 + - - -
881D GLU* 4.4 12.1 - - + +
882D GLY* 3.4 33.5 + - - +
885D LYS* 3.3 30.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il